Synthetic scaffolds for pathway enhancement
Tài liệu tham khảo
Nicolaou, 2010, A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: from biofuels and chemicals, to biocatalysis and bioremediation, Metab Eng, 12, 307, 10.1016/j.ymben.2010.03.004
Jiang, 2005, Metabolic engineering of the phenylpropanoid pathway in Saccharomyces cerevisiae, Appl Environ Microbiol, 71, 2962, 10.1128/AEM.71.6.2962-2969.2005
Menon, 2008, Halothiobacillus neapolitanus carboxysomes sequester heterologous and chimeric RubisCO species, PLoS ONE, 3
Bülow, 1987, Characterization of an artificial bifunctional enzyme, beta-galactosidase/galactokinase, prepared by gene fusion, Eur J Biochem, 163, 443, 10.1111/j.1432-1033.1987.tb10889.x
Conrado, 2008, Engineering the spatial organization of metabolic enzymes: mimicking nature's synergy, Curr Opin Biotechnol, 19, 492, 10.1016/j.copbio.2008.07.006
Lee, 2012, Spatial organization of enzymes for metabolic engineering, Metab Eng, 14, 242, 10.1016/j.ymben.2011.09.003
Na, 2010, Construction and optimization of synthetic pathways in metabolic engineering, Curr Opin Microbiol, 13, 363, 10.1016/j.mib.2010.02.004
Meynial Salles, 2007, Evolution of a Saccharomyces cerevisiae metabolic pathway in Escherichia coli, Metab Eng, 9, 152, 10.1016/j.ymben.2006.09.002
Wang, 2011, Metabolic engineering of Escherichia coli for α-farnesene production, Metab Eng, 13, 648, 10.1016/j.ymben.2011.08.001
Wilner, 2009, Self-assembly of enzymes on dna scaffolds: en route to biocatalytic cascades and the synthesis of metallic nanowires, Nano Lett, 9, 2040, 10.1021/nl900302z
Delebecque, 2011, Organization of intracellular reactions with rationally designed RNA assemblies, Science, 333, 470, 10.1126/science.1206938
Parsons, 2008, Biochemical and structural insights into bacterial organelle form and biogenesis, J Biol Chem, 283, 14366, 10.1074/jbc.M709214200
Miles, 1999, The molecular basis of substrate channeling, J Biol Chem, 274, 12193, 10.1074/jbc.274.18.12193
Bayer, 2004, The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides, Annu Rev Microbiol, 58, 521, 10.1146/annurev.micro.57.030502.091022
Liu, 2013, Functional assembly of a multi-enzyme methanol oxidation cascade on a surface-displayed trifunctional scaffold for enhanced NADH production, Chem Commun (Camb), 49, 3766, 10.1039/c3cc40454d
Dueber, 2009, Synthetic protein scaffolds provide modular control over metabolic flux, Nat Biotechnol, 27, 753, 10.1038/nbt.1557
Moon, 2010, Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli, Metab Eng, 12, 298, 10.1016/j.ymben.2010.01.003
Whitaker, 2011, Metabolic pathway flux enhancement by synthetic protein scaffolding, Methods Enzymol, 497, 447, 10.1016/B978-0-12-385075-1.00019-6
You, 2012, Facilitated substrate channeling in a self-assembled trifunctional enzyme complex, Angew Chemie – Int Ed, 51, 8787, 10.1002/anie.201202441
Bauler, 2010, Channeling by proximity: the catalytic advantages of active site colocalization using brownian dynamics, J Phys Chem Lett, 1, 1332, 10.1021/jz1002007
Castellana, 2014, Enzyme clustering accelerates processing of intermediates through metabolic channeling, Nat Biotechnol, 32, 1011, 10.1038/nbt.3018
Gao, 2014, Artificial multienzyme supramolecular device: highly ordered self-assembly of oligomeric enzymes in vitro and in vivo, Angew Chemie Int Ed, 53, 14027, 10.1002/anie.201405016
Pinheiro, 2011, Challenges and opportunities for structural DNA nanotechnology, Nat Nanotechnol, 6, 763, 10.1038/nnano.2011.187
Linko, 2013, The enabled state of DNA nanotechnology, Curr Opin Biotechnol, 24, 555, 10.1016/j.copbio.2013.02.001
Wilner, 2009, Enzyme cascades activated on topologically programmed DNA scaffolds, Nat Nanotechnol, 4, 249, 10.1038/nnano.2009.50
Fu, 2012, Interenzyme substrate diffusion for an enzyme cascade organized on spatially addressable DNA nanostructures, J Am Chem Soc, 134, 5516, 10.1021/ja300897h
Conrado, 2012, DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency, Nucleic Acids Res, 40, 1879, 10.1093/nar/gkr888
Lee, 2013, Improved production of l-threonine in Escherichia coli by use of a DNA scaffold system, Appl Environ Microbiol, 79, 774, 10.1128/AEM.02578-12
Liu, 2014, Spatial modulation of key pathway enzymes by DNA-guided scaffold system and respiration chain engineering for improved N-acetylglucosamine production by Bacillus subtilis, Metab Eng, 24, 61, 10.1016/j.ymben.2014.04.004
Sachdeva, 2014, In vivo co-localization of enzymes on RNA scaffolds increases metabolic production in a geometrically dependent manner, Nucleic Acids Res, 42, 9493, 10.1093/nar/gku617
Delebecque, 2012, Designing and using RNA scaffolds to assemble proteins in vivo, Nat Protoc, 7, 1797, 10.1038/nprot.2012.102
Negi, 2008, New redesigned zinc-finger proteins: design strategy and its application, Chem – A Eur J, 14, 3236, 10.1002/chem.200701320
Chen, 2014, Biomolecular scaffolds for enhanced signaling and catalytic efficiency, Curr Opin Biotechnol, 28, 59, 10.1016/j.copbio.2013.11.007
DeLoache, 2013, Compartmentalizing metabolic pathways in organelles, Nat Biotechnol, 31, 320, 10.1038/nbt.2549
Chen, 2012, Designing biological compartmentalization, Trends Cell Biol, 22, 662, 10.1016/j.tcb.2012.07.002
Kim, 2013, Engineering nanoscale protein compartments for synthetic organelles, Curr Opin Biotechnol, 24, 627, 10.1016/j.copbio.2012.11.012
Cheng, 2008, Bacterial microcompartments: their properties and paradoxes, BioEssays, 30, 1084, 10.1002/bies.20830
Chowdhury, 2014, Diverse bacterial microcompartment organelles, Microbiol Mol Biol Rev, 78, 438, 10.1128/MMBR.00009-14
Parsons, 2010, Synthesis of empty bacterial microcompartments, directed organelle protein incorporation, and evidence of filament-associated organelle movement, Mol Cell, 38, 305, 10.1016/j.molcel.2010.04.008
Fan, 2010, Short N-terminal sequences package proteins into bacterial microcompartments, Proc Natl Acad Sci U S A, 107, 7509, 10.1073/pnas.0913199107
Choudhary, 2012, Engineered protein nano-compartments for targeted enzyme localization, PLoS ONE, 7
Wörsdörfer, 2011, Directed evolution of a protein container, Science, 331, 589, 10.1126/science.1199081
Avalos, 2013, Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols, Nat Biotechnol, 31, 335, 10.1038/nbt.2509
Rhee, 2011, Colorful virus-like particles: fluorescent protein packaging by the Qβ capsid, Biomacromolecules, 12, 3977, 10.1021/bm200983k
Quellec, 1999, Protein encapsulation within poly(ethylene glycol)-coated nanospheres. II. Controlled release properties, J Biomed Mater Res, 47, 388, 10.1002/(SICI)1097-4636(19991205)47:3<388::AID-JBM14>3.0.CO;2-V
Colletier, 2002, Protein encapsulation in liposomes: efficiency depends on interactions between protein and phospholipid bilayer, BMC Biotechnol, 2, 9, 10.1186/1472-6750-2-9
O’Neil, 2011, Genetically programmed in vivo packaging of protein cargo and its controlled release from bacteriophage P22, Angew Chemie – Int Ed, 50, 7425, 10.1002/anie.201102036
Patterson, 2012, Nanoreactors by programmed enzyme encapsulation inside the capsid of the bacteriophage P22, ACS Nano, 6, 5000, 10.1021/nn300545z
Patterson, 2014, Encapsulation of an enzyme cascade within the bacteriophage P22 virus-like particle, ACS Chem Biol, 9, 359, 10.1021/cb4006529
Moon, 2009, Production of glucaric acid from a synthetic pathway in recombinant Escherichia coli, Appl Environ Microbiol, 75, 589, 10.1128/AEM.00973-08
Pitera, 2007, Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli, Metab Eng, 9, 193, 10.1016/j.ymben.2006.11.002
Pfleger, 2006, Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes, Nat Biotechnol, 24, 1027, 10.1038/nbt1226
Golding, 2004, RNA dynamics in live Escherichia coli cells, Proc Natl Acad Sci U S A, 101, 11310, 10.1073/pnas.0404443101
Qi, 2014, A versatile framework for microbial engineering using synthetic non-coding RNAs, Nat Rev Microbiol, 12, 341, 10.1038/nrmicro3244